Figure 2.

Hierarchical clustering and functional classification of differentially expressed
genes. Genome-wide expression analysis was performed for two different experimental
groups (G) of chondrocytes stimulated with supernatant of a synovial fibroblast cell
line derived from a patient with rheumatoid arthritis (RASFsn) and chondrocytes stimulated
with supernatant of a synovial fibroblast cell line derived from normal donor (NDSFsn)
(n = 2). Each experimental group was a pool of RNA isolated from stimulated chondrocytes
that originated from three different donors; that is, group 1 (G1) consisted of equal
amounts of RNA from stimulated chondrocytes of donors 1 to 3 and group 2 (G2) of donors
4 to 6. Genes that displayed ≥2-fold increase or ≤-2-fold decrease in RASFsn-stimulated
compared with NDSFsn-stimulated chondrocytes determined by both analyses with GeneChip
Operating Software and Robust Multi-array Analysis were hierarchically clustered and
functionally classified into six groups. Colors represent relative levels of gene
expression: bright red indicates the highest level of expression and bright green
indicates the lowest level of expression. Expression data from the different experimental
groups were compared and showed that the expression patterns were similar for the
corresponding experimental groups of both RASFsn-stimulated and NDSFsn-stimulated
chondrocytes because they clustered and were therefore most similar to each other,
showing little variability.